You can place your rewrite rules in the nginx Directives field on the Options tab of a website in ISPConfig. Of course, the Options tab is accessible only for admin to avoid people placing rubbish in that field (which would prevent nginx from starting...).

I still don't know how client can use htaccess. Accoring to nginx http://wiki.nginx.org/LikeApache-htaccess it does not support htaccess, so that means that somehow i have to specially add some configuration so nginx would read htaccess file.